Introduction

All code associated to this page can be foundhere

Ulcerative colitis (UC) is one of the two main forms of Inflammatory bowel disease, a chronic inflammatory condition where the colon and rectum become inflammed. UC is characterized by the presence of small ulcers in the lining of the colon´s lining, as well as a variety of symptoms, including abdominal pain, diarrhea, or weight loss.

As a disease associated with immune cell responses, UC is characterized by a complex de-regulation of innate and adaptive immune cell activity, that includes as main features the overactivation of neutrophiles and a Th2-like profile (e.g. see here).

Whereas an important corpus of data has been collected about the pathology of UC immune responses, key questions, such as the interaction between the gut microbiota and the immune cells, or whether disfunctions in the epithelial barrier are a cause or a consequence of altered immune responses, remain unanswered. Transcriptomic analyses of single cells or whole pieces of tissue have helped to clarify these issues (examples can be found here or here).

Raw counts matrix

Sample metadata

Patient IDs

157
877
1057
1077
1192
1214
8854
8855
8874
8878
8879
8881

Area from which samples were obtained

Ascending
Descending
Large
Rectum
Sigmoid
Tranverse

Lognormalization of counts

Most variable genes

Mean vs CoV for all genes

Mean vs CoV for most variable genes

Principal component analysis (PCA)

PCA with all genes

Scree plot

PCA Scores

PCA with 500 most variable genes

PCA Scores

Differential expression analysis

GO enrichment up and down-regulated genes

Heatmap top 50 DEGs

Based on p.adj

Z-score norm

Plot single genes

standardGeneric for "plot" defined from package "base"

function (x, y, ...) 
standardGeneric("plot")
<environment: 0x00000200332a3ea0>
Methods may be defined for arguments: x, y
Use  showMethods(plot)  for currently available ones.